First, I'm no fiberglass expert, but, I am just a few weeks ahead of you in building my Pygmy Artic Turn and recently did my fill coats also. Two things I learned:

1. The bubbles do not fill in later. You have to cut them down now and make sure that the epoxy saturates everywhere. It sounds like you did this. I did this in a few small spots that would not lay flat. I used a box cutter and made a small slit before the epoxy was dry (just tacky still) and then layed the glass flat and made sure there was plenty of epoxy there.

2. I chose to not sand between coats. I was more afraid of cutting through the glass with the sander and weakening the boat than I was about a few blemishes. That was my choice but I could definately understand that some people may be much more of a perfectionist than I am. Afer the fill coats you could hardly notice anything. I am sure that after a final sanding and varnish these small craters will not be noticable.

The only blemishes that still is noticable is one small spot on the cutwater that had air under it. I have decided to leave it alone for now.

The point is: you really can't see these bumps afer a few fill coats.